Assessing the Conservation of Mammalian Gene Expression

Using High-density Exon Arrays

 

Yi Xing^1,2,*, Zhengqing Ouyang³, Karen Kapur², Matthew P. Scott⁴, Wing Hung Wong^2,*

¹Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
²Department of Statistics, Stanford University, Stanford, California 94305, USA
³Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA
⁴Departments of Developmental Biology, Genetics, and Bioengineering, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305, USA 

*To whom correspondence should be addressed.  
E-mail: yi-xing@uiowa.edu; whwong@stanford.edu.

 

Abstract

Microarray data from multiple species have been used to study evolutionary constraints on gene expression.  Expression measurements from conventional microarray platforms such as the 3' expression arrays are strongly affected by platform-dependent probe effects that may introduce apparent, but misleading discrepancies between species. In this manuscript, we assess the conservation of mammalian gene expression in adult tissues using data from a high-density exon array platform. The exon arrays have more than six million probes on a single array targeting all exons in a genome.  We find that, unlike 3' array data, gene expression measurements from exon arrays reveal patterns of gene expression that are highly conserved between humans and mice in multiple tissues. Our analysis provides strong evidence for widespread stabilizing selection pressure on transcript abundance during mammalian evolution.

 

Supplementary Data

Exon Array expression indexes for human tissues: GeneBASE results; PLIER results; Gene information file.

Exon Array expression indexes for mouse tissues: GeneBASE results; PLIER results; Gene information file.

 

References

Xing, Y., Kapur, K., Wong, WH. (2006) Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE, 1(1):e88.

Xing, Y.*, Ouyang, Z., Kapur, K., Scott, MP., Wong, WH*. (2007) Molecular Biology and Evolution, In press.